Class: HQMF2::DataCriteria

Inherits:
Object
  • Object
show all
Includes:
Utilities
Defined in:
lib/hqmf-parser/2.0/data_criteria.rb

Overview

Represents a data criteria specification

Constant Summary collapse

VARIABLE_TEMPLATE = 
"0.1.2.3.4.5.6.7.8.9.1"
SATISFIES_ANY_TEMPLATE = 
"0.1.2.3.4.5.6.7.8.9.2"
SATISFIES_ALL_TEMPLATE = 
"0.1.2.3.4.5.6.7.8.9.3"
CONJUNCTION_CODE_TO_DERIVATION_OP = 
{
  'OR' => 'UNION',
  'AND' => 'XPRODUCT'
}
CRITERIA_GLOB = 
"*[substring(name(),string-length(name())-7) = \'Criteria\']"

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Utilities

#attr_val, attr_val, #to_xml

Methods included from HQMF::Conversion::Utilities

#build_hash, #check_equality, #json_array, #openstruct_to_json

Constructor Details

#initialize(entry) ⇒ DataCriteria

Create a new instance based on the supplied HQMF entry

Parameters:

  • entry (Nokogiri::XML::Element) —

    the parsed HQMF entry



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 26

def initialize(entry)
  @entry = entry
  @local_variable_name = extract_local_variable_name
  @status = attr_val('./*/cda:statusCode/@code')
  @description = attr_val("./#{CRITERIA_GLOB}/cda:text/@value")
  extract_negation()
  extract_specific_or_source()
  @effective_time = extract_effective_time
  @temporal_references = extract_temporal_references
  @derivation_operator = extract_derivation_operator
  @field_values = extract_field_values
  @subset_operators = extract_subset_operators
  @children_criteria = extract_child_criteria
  @id_xpath = './*/cda:id/@extension'
  @code_list_xpath = './*/cda:code'
  @value_xpath = './*/cda:value'
  @comments = @entry.xpath("./#{CRITERIA_GLOB}/cda:text/cda:xml/cda:qdmUserComments/cda:item/text()", HQMF2::Document::NAMESPACES).map{ |v| v.content }
  @variable = false

  # Try to determine what kind of data criteria we are dealing with
  # First we look for a template id and if we find one just use the definition
  # status and negation associated with that
  if !extract_type_from_template_id()
    # If no template id or not one we recognize then try to determine type from
    # the definition element
    extract_type_from_definition()
  end
  
  patch_xpaths_for_criteria_type()
end

Instance Attribute Details

#children_criteria ⇒ Object (readonly)

Returns the value of attribute children_criteria.



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 8

def children_criteria
  @children_criteria
end

#comments ⇒ Object (readonly)

Returns the value of attribute comments.



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 11

def comments
  @comments
end

#derivation_operator ⇒ Object (readonly)

Returns the value of attribute derivation_operator.



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 9

def derivation_operator
  @derivation_operator
end

#description ⇒ Object (readonly)

Returns the value of attribute description.



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 9

def description
  @description
end

#effective_time ⇒ Object (readonly)

Returns the value of attribute effective_time.



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 7

def effective_time
  @effective_time
end

#field_values ⇒ Object (readonly)

Returns the value of attribute field_values.



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 10

def field_values
  @field_values
end

#is_source_data_criteria ⇒ Object (readonly)

Returns the value of attribute is_source_data_criteria.



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 11

def is_source_data_criteria
  @is_source_data_criteria
end

#negation ⇒ Object (readonly)

Returns the value of attribute negation.



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 9

def negation
  @negation
end

#negation_code_list_id ⇒ Object (readonly)

Returns the value of attribute negation_code_list_id.



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 9

def negation_code_list_id
  @negation_code_list_id
end

#property ⇒ Object (readonly)

Returns the value of attribute property.



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 7

def property
  @property
end

#section ⇒ Object (readonly)

Returns the value of attribute section.



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 7

def section
  @section
end

#source_data_criteria ⇒ Object (readonly)

Returns the value of attribute source_data_criteria.



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 10

def source_data_criteria
  @source_data_criteria
end

#specific_occurrence ⇒ Object (readonly)

Returns the value of attribute specific_occurrence.



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 11

def specific_occurrence
  @specific_occurrence
end

#specific_occurrence_const ⇒ Object (readonly)

Returns the value of attribute specific_occurrence_const.



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 10

def specific_occurrence_const
  @specific_occurrence_const
end

#status ⇒ Object (readonly)

Returns the value of attribute status.



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 7

def status
  @status
end

#subset_operators ⇒ Object (readonly)

Returns the value of attribute subset_operators.



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 8

def subset_operators
  @subset_operators
end

#temporal_references ⇒ Object (readonly)

Returns the value of attribute temporal_references.



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 8

def temporal_references
  @temporal_references
end

#type ⇒ Object (readonly)

Returns the value of attribute type.



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 7

def type
  @type
end

#value ⇒ Object (readonly)

Returns the value of attribute value.



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 7

def value
  @value
end

Instance Method Details

#code_list_id ⇒ String

Get the code list OID of the criteria, used as an index to the code list database

Returns:

  • (String) —

    the code list identifier of this data criteria



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 199

def code_list_id
  attr_val("#{@code_list_xpath}/@valueSet")
end

#extract_local_variable_name ⇒ Object 



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 83

def extract_local_variable_name
  lvn = @entry.at_xpath("./cda:localVariableName")
  lvn["value"] if lvn
end

#extract_type_from_definition ⇒ Object 



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 88

def extract_type_from_definition
  if @entry.at_xpath("./cda:grouperCriteria") 
    if @local_variable_name && @local_variable_name.match(/qdm_/)
      @variable = true
    end
    @definition = 'derived'
    return 
  end
  # See if we can find a match for the entry definition value and status.
  entry_type = attr_val('./*/cda:definition/*/cda:id/@extension')
  begin
    settings = HQMF::DataCriteria.get_settings_for_definition(entry_type, @status)
    @definition = entry_type
  rescue
    # if no exact match then try a string match just using entry definition value
    case entry_type
    when 'Problem', 'Problems'
      @definition = 'diagnosis'
    when 'Encounter', 'Encounters'
      @definition = 'encounter'
    when 'LabResults', 'Results'
      @definition = 'laboratory_test'
    when 'Procedure', 'Procedures'
      @definition = 'procedure'
    when 'Medication', 'Medications'
      @definition = 'medication'
      if !@status
        @status = 'active'
      end
    when 'RX'
      @definition = 'medication'
      if !@status
        @status = 'dispensed'
      end
    when 'Demographics'
      @definition = definition_for_demographic
    when 'Derived'
      @definition = 'derived'
    when nil
      @definition = 'variable'
    else
      raise "Unknown data criteria template identifier [#{entry_type}]"
    end
  end
end

#extract_type_from_template_id ⇒ Object 



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 134

def extract_type_from_template_id
  template_ids = @entry.xpath('./*/cda:templateId/cda:item', HQMF2::Document::NAMESPACES).collect do |template_def|
    HQMF2::Utilities.attr_val(template_def, '@root')
  end
  if template_ids.include?(HQMF::DataCriteria::SOURCE_DATA_CRITERIA_TEMPLATE_ID)
    @is_source_data_criteria = true
  end
  found = false
  template_ids.each do |template_id|
    defs = HQMF::DataCriteria.definition_for_template_id(template_id)
    
    if defs
      @definition = defs['definition']
      @status = defs['status'].length > 0 ? defs['status'] : nil
      @negation = defs['negation']
      found ||= true
    elsif template_id == VARIABLE_TEMPLATE
      @derivation_operator = HQMF::DataCriteria::INTERSECT if @derivation_operator == HQMF::DataCriteria::XPRODUCT
      @definition ||= 'derived'
      @negation = false
      @variable = true
      found ||= true
    elsif template_id == SATISFIES_ANY_TEMPLATE
      @definition = HQMF::DataCriteria::SATISFIES_ANY
      @negation = false
      return true
    elsif template_id == SATISFIES_ALL_TEMPLATE
      @definition = HQMF::DataCriteria::SATISFIES_ALL
      @derivation_operator = HQMF::DataCriteria::INTERSECT
      @negation = false
      found ||= true
    end
  end
  found
end

#id ⇒ String

Get the identifier of the criteria, used elsewhere within the document for referencing

Returns:

  • (String) —

    the identifier of this data criteria



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 182

def id
  attr_val(@id_xpath)
end

#inline_code_list ⇒ Object 



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 203

def inline_code_list
  codeSystem = attr_val("#{@code_list_xpath}/@codeSystem")
  if codeSystem
    codeSystemName = HealthDataStandards::Util::CodeSystemHelper.code_system_for(codeSystem)
  else
    codeSystemName = attr_val("#{@code_list_xpath}/@codeSystemName")
  end
  codeValue = attr_val("#{@code_list_xpath}/@code")
  if codeSystemName && codeValue
    {codeSystemName => [codeValue]}
  else
    nil
  end
end

#patch_xpaths_for_criteria_type ⇒ Object 



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 57

def patch_xpaths_for_criteria_type  
  # Patch xpaths when necessary, HQMF data criteria are irregular in structure so
  # the same information is found in different places depending on the type of
  # criteria
  # Assumes @definition and @status are already set
  case @definition
  when 'transfer_to', 'transfer_from'
    @code_list_xpath = './cda:observationCriteria/cda:value'
  when 'diagnosis', 'diagnosis_family_history'
    @code_list_xpath = './cda:observationCriteria/cda:value'
  when 'physical_exam', 'risk_category_assessment', 'procedure_result', 'laboratory_test', 'diagnostic_study_result', 'functional_status_result', 'intervention_result'
    @value = extract_value
  when 'medication'
    case @status
    when 'dispensed', 'ordered'
      @code_list_xpath = './cda:supplyCriteria/cda:participation/cda:role/cda:code'
    else # active or administered
      @code_list_xpath = './cda:substanceAdministrationCriteria/cda:participation/cda:role/cda:code'
    end
  when 'patient_characteristic', 'patient_characteristic_birthdate', 'patient_characteristic_clinical_trial_participant', 'patient_characteristic_expired', 'patient_characteristic_gender', 'patient_characteristic_age', 'patient_characteristic_languages', 'patient_characteristic_marital_status', 'patient_characteristic_race'
    @value = extract_value
  when 'variable'
    @value = extract_value
  end
end

#title ⇒ String

Get the title of the criteria, provides a human readable description

Returns:

  • (String) —

    the title of this data criteria



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 188

def title
  dispValue = attr_val("#{@code_list_xpath}/cda:displayName/@value") 
  desc = nil
  if @description && (@description.include? ":")
     desc = @description.match(/.*:\s+(.+)/)[1]
  end
  dispValue || desc || id
end

#to_model ⇒ Object 



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 218

def to_model

  mv = value ? value.to_model : nil
  met = effective_time ? effective_time.to_model : nil
  mtr = temporal_references.collect {|ref| ref.to_model}
  mso = subset_operators.collect {|opr| opr.to_model}
  field_values = {}
  @field_values.each_pair do |id, val|
    field_values[id] = val.to_model
  end

  # Model transfers as a field
  if ['transfer_to', 'transfer_from'].include? @definition 
    field_values ||= {}
    field_code_list_id = @code_list_id
    if !field_code_list_id
      field_code_list_id = attr_val("./#{CRITERIA_GLOB}/cda:outboundRelationship/#{CRITERIA_GLOB}/cda:value/@valueSet")
    end
    field_values[@definition.upcase] = HQMF::Coded.for_code_list(field_code_list_id, title)
  end

  field_values = nil if field_values.empty?

  HQMF::DataCriteria.new(id, title, nil, description, code_list_id, children_criteria, 
    derivation_operator, @definition, status, mv, field_values, met, inline_code_list, 
    @negation, @negation_code_list_id, mtr, mso, @specific_occurrence, 
    @specific_occurrence_const, @source_data_criteria, @comments, @variable)
end

#to_s ⇒ Object 



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# File 'lib/hqmf-parser/2.0/data_criteria.rb', line 170

def to_s
  props = {
    :property => property,
    :type => type,
    :status => status,
    :section => section
  }
  "DataCriteria#{props.to_s}"
end